Epitope Scout
Identify and rank candidate surface epitopes on your target protein for de novo binder design. Upload a PDB or mmCIF structure, select a chain, and get scored epitope patches ready for RFdiffusion and BindCraft campaigns.
Free to use — create an account to get started. No credit card required.
From structure to scored epitopes in minutes
Upload structure
Provide a PDB or mmCIF file, or enter a PDB ID to fetch directly from RCSB.
Select target chain
Choose the chain you want to design binders against. Epitope Scout detects all available chains.
Automated analysis
RSA computation, spatial clustering, five-component scoring, quality flagging — all automated.
Ranked epitopes
Top 3 epitope patches scored 0–1, visualized in 3D, with downloadable CSV for RFdiffusion input.
Five-component composite score
Each candidate epitope patch is scored on a 0–1 scale combining five structural determinants from the protein-protein interaction literature. Higher scores indicate surfaces more suitable for de novo binder design.
Hydrophobic exposure
Hydrophobicity weighted by solvent accessibility. Measures the desolvation penalty — the thermodynamic driver of most protein-protein interactions.
Structural order
Secondary structure distribution. Beta-strands and alpha-helices provide rigid, preorganized interfaces that reduce the entropic cost of binding.
Rigidity
Crystallographic B-factor or AlphaFold pLDDT scores. Low flexibility means the surface is preorganized — less entropy to pay upon binding.
Surface accessibility
Inverted burial score. Flat, accessible surfaces are easier to engage with a designed binder scaffold than deep pockets or grooves.
Hot spot density
Fraction of known binding hot spot residues (Trp, Tyr, Arg, Phe). These amino acids contribute disproportionately to binding free energy at PPI interfaces.
Context that shapes your design strategy
PPI interface detection
Automatically detects natural protein-protein interaction interfaces from co-crystal structures. Shows which epitope patches overlap with known binding partner sites.
Known binder lookup
Queries SAbDab and RCSB for existing antibody and nanobody structures against your target. Shows contact residues so you can compare your epitope candidates to validated binding sites.
Quality flags
Non-scoring annotations flag potential concerns: loop-only anchors, all-polar patches, glycan proximity, high flexibility, and electrostatic asymmetry — so you know what to watch for.
The first step in any binder design campaign
Before running RFdiffusion or BindCraft, you need to know where on your target to direct the design. Hotspot selection is the single most consequential decision in a binder design campaign — it determines whether your generated scaffolds will engage a druggable, accessible surface or waste GPU hours on buried or disordered regions.
Epitope Scout replaces manual PyMOL inspection with a systematic, reproducible, literature-backed scoring approach. Run it before every campaign.
Starting a de novo binder design campaign and need to define hotspot residues
Evaluating multiple epitope regions on a target and need quantitative comparison
Working with a novel target with no known binders — need structural guidance
Preparing RFdiffusion or BindCraft input files and need residue selections
Reviewing a target structure before committing to a wet-lab campaign
Start identifying epitopes today
Create a free account and upload your first PDB structure. Scored epitope patches in minutes, ready for your next binder design campaign.